Research Article: Sequencing, genome analysis and prevalence of a cytorhabdovirus discovered in Carica papaya

Date Published: June 20, 2019

Publisher: Public Library of Science

Author(s): Andrés X. Medina-Salguero, Juan F. Cornejo-Franco, Samuel Grinstead, Dimitre Mollov, Joseph D. Mowery, Francisco Flores, Diego F. Quito-Avila, XianBing Wang.


The complete genome of a new rhabdovirus infecting papaya (Carica papaya L.) in Ecuador, named papaya virus E, was sequenced and characterized. The negative-sense single-stranded RNA genome consists of 13,469 nucleotides with six canonical open reading frames (ORFs) and two accessory short ORFs predicted between ORFs corresponding to P3 (movement protein) and M (matrix protein). Phylogenetic analyses using amino acid sequences from the nucleocapsid, glycoprotein and polymerase, grouped the virus with members of the genus Cytorhabdovirus, with rice stripe mosaic virus, yerba mate chlorosis-associated virus and Colocasia bobone disease-associated virus as closest relatives. The 3’ leader and 5’ trailer sequences were 144 and 167 nt long, respectively, containing partially complementary motifs. The motif 3’-AUUCUUUUUG-5’, conserved across rhabdoviruses, was identified in all but one intergenic regions; whereas the motif 3’-ACAAAAACACA-5’ was found in three intergenic junctions. This is the first complete genome sequence of a cytorhabdovirus infecting papaya. The virus was prevalent in commercial plantings of Los Ríos, the most important papaya producing province of Ecuador. Recently, the genome sequence of bean-associated cytorhabdovirus was reported. The genome is 97% identical to that of papaya virus E, indicating that both should be considered strains of the same virus.

Partial Text

The Rhabdoviridae, a negative-sense RNA virus family, contains viruses that infect a wide range of hosts including vertebrates, invertebrates and plants [1]. Virions have a helical, bullet-shape morphology, surrounded by a host-derived membrane [2]. Rhabdovirus genomes range from 11 to 16 kilobases (kb) with only non-segmented ones classically assigned to genera in the family. However, virus species with bipartite genomes have recently been included in the Rhabdoviridae [3,4].

The Rhabdoviridae is one of the most diverse virus families as it contains viruses that infect arthropods, vertebrates and plants [10]. Here, we present the characterization of a new rhabdovirus discovered from papaya plants in Ecuador. Aligning entire genomes of plant rhabdoviruses is difficult due to high divergence of sequences. Nevertheless, the evolutionary history of the virus was confidently inferred using single or concatenated alignments of the nucleocapsid, glycoprotein and polymerase amino acid sequences.